exercises:2017_ethz_mmm:stm
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exercises:2017_ethz_mmm:stm [2017/05/25 11:58] – created dpasserone | exercises:2017_ethz_mmm:stm [2020/08/21 10:15] (current) – external edit 127.0.0.1 | ||
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and copy there the tar file of the exercise: | and copy there the tar file of the exercise: | ||
< | < | ||
- | cp /home/cpi/exercise_11.tar ./ | + | cp /home/cpi/exercise_12.tar ./ |
- | tar -xvf exercise_11.tar | + | tar -xvf exercise_12.tar |
- | cd exercise_11 | + | cd exercise_12 |
</ | </ | ||
+ | </ | ||
+ | |||
+ | We consider two possible chemical terminations for a finite size 7-AGNR. | ||
+ | In TASK_1 the ribbon is terminated with a C-H2 bonding while in TASK_2 the termination is C-H | ||
+ | The additional H atom present at the termini of the ribbon of TASK_1 will suppress the spin polarized | ||
+ | edge states that are evident in the ribbon of TASK_2 | ||
+ | |||
+ | |||
+ | ===TASK_1=== | ||
+ | Have a look to the cp2k input file cp2k.inp | ||
+ | used to obtain quickly the optimized geometry of a ribbon adsorbed on a Au substrate. | ||
+ | The ribbon is modelled within DFTB (similar to tight binding) while the substrate is modelled | ||
+ | via Embedded Atom Model. | ||
+ | An empirical potential in teh form of C6/R^6 plus a pauli repulsion | ||
+ | is added to couple the adsorbate/ | ||
+ | |||
+ | |||
+ | Two geometry fiels are present: mol.xyz and all.xyz | ||
+ | The input needs both of them. | ||
+ | |||
+ | Have a look at the geometry of the system using ASE: | ||
+ | |||
+ | < | ||
+ | ipython | ||
+ | In [1]: from ase.io import read | ||
+ | |||
+ | In [2]: from ase.visualize import view | ||
+ | |||
+ | In [3]: s=read(" | ||
+ | |||
+ | In [4]: view(s) | ||
+ | |||
+ | In [5]: exit() | ||
+ | </ | ||
+ | |||
+ | <note important> | ||
+ | submit the geometry optimization run | ||
+ | < | ||
+ | qsub run | ||
+ | </ | ||
+ | |||
+ | After completion of the optimization you should extract the final coordinates of the molecule | ||
+ | and copy them in the STM directory to compute the KS orbitals and to ocmpute the STM images | ||
+ | you can extract the coordinates running the following script: | ||
+ | < | ||
+ | ./pos.sc | ||
+ | </ | ||
+ | </ | ||
+ | |||
+ | Now go to the STM directory andsubmit the run script | ||
+ | < | ||
+ | qsub run | ||
+ | </ | ||
+ | The program will compute the 10 highest and 10 lowest KS orbitals. | ||
+ | You can produce a contour plot of each orbital on a plane ~2A above the ribbon running a pyhton script: | ||
+ | |||
+ | < | ||
+ | ./ | ||
+ | </ | ||
+ | I will also show you how to visualize the orbitals with VMD. | ||
+ | |||
+ | To obtain teh stm images you have to combine different KS orbitals (depending on the bias voltage applied) | ||
+ | into a single cube file: | ||
+ | |||
+ | < | ||
+ | qsub run_sumbias | ||
+ | </ | ||
+ | you will then obtain a cube file for each desired bias voltage (see the script run_sumbias) | ||
+ | |||
+ | Now you can compuyte a constant current STM image runnong the script | ||
+ | |||
+ | < | ||
+ | qsub run_stm | ||
+ | </ | ||
+ | |||
+ | Please note that we are simulating a molecule, we do not include the electrons of the substrate | ||
+ | thus we have a disceret spectrum of energies and it is quite likely that for values of the bias voltage | ||
+ | that fall in the HOMO-LUMO gap we will obtain an empty image | ||
+ | |||
+ | Now we can simulate for teh same ribbon a AFM image: | ||
+ | Go the the AFM directory of TASK_1 | ||
+ | copy there the p.xyz file that you find in the STM directory | ||
+ | and execute: | ||
+ | |||
+ | < | ||
+ | ./run_PP | ||
+ | </ | ||
+ | It will take ~ 5 minutes, then you will find a dir containing the AFM simulated image. | ||
+ | |||
+ | ===TASK_2=== | ||
+ | Repeat all the instructions of TASK_1 for the scripts present in the dir TASK_2 | ||
+ | <note warning> | ||
+ | Be carefulhere we do a spin polarized simulation, | ||
+ | we have to distinguish the three C atoms of one terminus of the ribbon from the | ||
+ | three of the opposite terminus calling them C1 and C2. | ||
+ | |||
+ | When the file p.xyz is created in the STM dir (after running ./pos.sc) | ||
+ | copy it immediateli to the AFM dir. | ||
+ | Now, before executing the instructions for the STM dir | ||
+ | edit the file p.xyz and modify it in such a way that | ||
+ | the first three C atoms will be labelled as C1 | ||
+ | and the C atoms from 4 to 6 will be labelled as C2 | ||
+ | < | ||
+ | 222 | ||
+ | |||
+ | C1 6.0848407282 | ||
+ | C1 6.0865671686 | ||
+ | C1 6.1020007836 | ||
+ | C2 | ||
+ | C2 | ||
+ | C2 | ||
+ | H | ||
+ | H | ||
+ | </ | ||
+ | |||
+ | </ | ||
+ | |||
+ | <note important> | ||
+ | Notice the difference between the images in TASK_2 and the images in TASK_1 | ||
+ | In TASK_2 we have KS states localised at the termini of the ribbon. | ||
+ | These states are suppressed by the addiitonal H atoms in TASK_1 | ||
+ | </ | ||
+ |
exercises/2017_ethz_mmm/stm.1495713519.txt.gz · Last modified: 2020/08/21 10:15 (external edit)